Inbreeding depression is widely recognized as a near-universal phenomenon of high conservation concern, particularly as wild populations continue to decline. However, most research to date has focused on early life stages, leaving later-life effects comparatively understudied, especially for wild populations of long-lived species. The Pyrenean brown bear (Ursus arctos), characterized by a small population, high levels of inbreeding, and conflicts with human activities, embodies the conservation challenges faced by many large mammals. We analyzed 27 years of monitoring data to quantify inbreeding depression across multiple life stages on survival, reproduction and dispersal. Our results reveal strong inbreeding depression effects, particularly in early life stages, including reduction in litter size and in natal dispersal distance. In adults, more inbred mothers exhibit lower cub survival. The cumulative effect of inbreeding, as measured by lifetime breeding success, also shows a negative impact. These findings highlight the necessity of assessing inbreeding depression across the entire life cycle to accurately evaluate its threat to population dynamics and viability. Such comprehensive assessments will become increasingly essential for wild plant and animal populations constrained by habitat destruction, human-wildlife conflict, and harvesting pressures.

README for the paper: Inbreeding depression across multiple life history traits in a long-lived mammal

GENETIC DATA

Dataset: genotypes_founders_new_set.txt

File Format:

Name: genotypes_founders_new_set.txt
Type: txt 
Delimiter: tabulation

This dataset gives the genotypes for 23 microsatellite markers of 9 founders of the population. The missing values are coded as 0.

Dataset: genotypes_founders_old_set.txt

File Format:

Name: genotypes_founders_old_set.txt
Type: txt 
Delimiter: tabulation

This dataset gives the genotypes for 11 microsatellite markers of 8 founders of the population. The missing values are coded as 0.

DEMOGRAPHIC DATA

Dataset: litter_size_dt.csv
File Format:

Name: litter_size_dt.csv
Type: CSV (Comma-Separated Values)
Delimiter: ,

Variables description:

-Birth_year (numeric): Year of birth of the bear.    
-Id_mother (categorical): Anonymized identifier of the mother of the bear.
-Litter_size (numeric): Number of cubs in the litter.
-Id_father (categorical): Anonymized identifier of the father of the bear.
-Inbreeding_individual (numeric): Inbreeding coefficient of the cubs from the litter.
-Primiparity (categorical): Whether the litter was the mother’s first. True if the litter is the first one detected for the mother otherwise False.
-Inbreeding_mother (numeric): Inbreeding coefficient of the mother of the bear calculated from the pedigree, with the relatedness of the founders and half-founders corrected by microsatellite data.
-Mother_age (numeric): Age of the mother in the year of the litter’s birth.
-Complete_litter (categorical): True if all the cubs from the litter have been genotyped and therefore have a known father.
-Diff_detect_litter (numeric): Time is measured as the number of days between March 15 of the birth year and the detection of the litter, which allowed for determining its size (i.e, picture or direct observation).
-Male_density (numeric): Number of adult males with overlapping home range with the mother at the year of the litter’s birth.

Dataset: survival_dt.csv
File Format:

Name: survival_dt.csv
Type: CSV (Comma-Separated Values)
Delimiter: ,

Variables description:

-Id_bear (categorical): Anonymized identifier of bears.
-Sex (categorical): Sex of the bear (M = Male, F = Female).
-X1996 to X2023: Detection status of the bear for each year. 0 indicates no detection, 1 a detection of the bear alive, 2 a dead recovery of the bear only and 3 a detection of the bear alive followed by a dead recovery that year.
-Inbreeding_individual (numeric): Inbreeding coefficient of the bear calculated from the pedigree, with the relatedness of the founders and half-founders corrected by microsatellite data. Some litters have not been genotyped, resulting in missing inbreeding coefficient values (NA) for those individuals. 
-Inbreeding_mother (numeric): Inbreeding coefficient of the mother of the bear calculated from the pedigree, with the relatedness of the founders and half-founders corrected by microsatellite data. As the mother is unknown for founders, the inbreeding of mother is missing (NA values).
-Age_first_detection (numeric): Age of the bear when it was first detected.

Dataset: Natal_dispersal_dist.csv
File Format:

Name: Natal_dispersal_dist.csv
Type: CSV (Comma-Separated Values)
Delimiter: ,

Variables description:

-Id_bear (categorical): Anonymized identifier of bears.
-Id_mother (categorical): Anonymized identifier of the mother of the bear.
-Sex (categorical): Sex of the bear (M = Male, F = Female).
-Sexual_maturity (numeric): Year when theoretical sexual maturity is reached for the bear (3 years old).
-Inbreeding_individual (numeric): Inbreeding coefficient of the bear calculated from the pedigree, with the relatedness of the founders and half-founders corrected by microsatellite data.
-Distance (numeric): Shortest distance in meters between the centroids of the natal and adult home ranges on the WGS84 ellipsoid.
-Mother_age (numeric): Age of the mother in the year of the litter birth.
-Number_cubs (numeric): Number of cubs in the litter of the bear.
-Nb_points (numeric): Number of samples associated with spatial coordinates used to define the centroid of the adult home range.

Dataset: Age_first_repro.csv
File Format:

Name: Age_first_repro.csv
Type: CSV (Comma-Separated Values)
Delimiter: ,

Variables description:

-Id_bear (categorical): Anonymized identifier of bears.
-Sex (categorical): Sex of the bear (M = Male, F = Female).
-Inbreeding_individual (numeric): Inbreeding coefficient of the bear calculated from the pedigree, with the relatedness of the founders and half-founders corrected by microsatellite data.
-Age_first_repro (numeric): Age of the bear at the first successful copulation, defined as one year before the first cubs are detected. If the bear never reproduced, the value is missing (NA).
-Reproduction (categorical): Indicates whether the bear reproduced successfully: True if cubs were detected, False otherwise.
-Number_potential_repro_partner (numeric): Number of adult bears (older than 3 years old) from the opposite sex with an overlapping home range at the year of sexual maturity (3 years old).
-First_Reproduction_censored (numeric): If the bear has a reproduction detected: age of the bear at the first successful copulation otherwise, the number of years of monitoring without reproduction (from birth to last observation).

Dataset: yearly_breeding_success_dt.csv
File Format:

Name: yearly_breeding_success_dt.csv
Type: CSV (Comma-Separated Values)
Delimiter: ,

Variables description:

-Id_bear (categorical): Anonymized identifier of bears.
-Sex (categorical): Sex of the bear (M = Male, F = Female).
-Inbreeding_individual (numeric): Inbreeding coefficient of the bear calculated from the pedigree, with the relatedness of the founders and half-founders corrected by microsatellite data.
-Year (numeric): Year when the number of cubs produced is measured
-Nb_repro_year_cub (numeric): Number of offspring detected each year over an individual’s reproductive period (from the age of two until the last observed year of the individual’s life, removing for females, the first year after they were observed with cubs). 
-Number_potential_repro_partner (numeric): Number of adult bears (older than 3 years old) from the opposite sex with an overlapping home range in the year of sexual maturity (3 years old).
-Age (numeric): Age of the bear at the year of birth of the cubs
-Age_2 (numeric): Age of the bear at the year of birth of the cubs to the power of two

Dataset: life_time_breeding_success.csv
File Format:

Name: life_time_breeding_success.csv
Type: CSV (Comma-Separated Values)
Delimiter: ,

Variables description:

-Id_bear (categorical): Anonymized identifier of bears. If the bear is a cub added to complete a litter to three cubs, the value is missing (NA).
-Id_mother (categorical): Anonymized identifier of the mother of the bear.
-Birth_year (numeric): Year of birth of the bear.
-Inbreeding_individual (numeric): Inbreeding coefficient of the bear calculated from the pedigree, with the relatedness of the founders and half-founders corrected by microsatellite data.
-number_cubs (numeric): The number of a bear's offspring that survived to at least one year old
-Additional_cubs (categorical): True if the cub was observed, False if the cub was never observed but added to fill each litter to three offspring to take into account cubs that may have died before being detected and the potential impact of inbreeding on litter size.
-censored (categorical): 0 if the bear was dead at the end of the data sample (2023), 1 otherwise.

Script: RScript

File Format:

Name: RScript.R
Type: R (version 4.3.3)

Purpose:

The R script reproduces the analyses performed in the paper "Inbreeding depression across multiple life history traits in a long-lived mammal". It includes:

-Data Preparation (Standardizing numerical predictors, filtering data to create subsets for specific analyses (e.g., capture-mark-recapture analyses), etc.), 
-Model Building
-Diagnostics and Model Checking: checking multicollinearity and residual diagnostics with the DHARMa package.

Data from: Inbreeding depression across multiple life history traits in a long-lived mammal

Data files

Abstract